Under the dual pressure of economic development and environmental protection, it is urgent that we improve the efficiency of green innovation. Enterprise digital transformation brings opportunities to improve the efficiency of green innovation. However, most current studies focus on the relationship between the two from the micro level, ignoring the impact of enterprise digital transformation on the green innovation of other innovation entities within the region, and have not yet described it in detail from the perspective of digital capabilities. Therefore, based on Chinese data, this paper studies the impact of enterprise digital transformation on regional green innovation efficiency from the perspective of digital capability, and provides a theoretical reference for improving regional green innovation efficiency. The research shows that (1) the digital capabilities of enterprise digital transformation include digital acquisition capability, digital utilization capability, and digital sharing capability, which have significant promoting effects on regional green innovation efficiency; (2) strengthening information resources, knowledge resources, R&D funds, and human resources are the role channels indicated by mechanism analysis; (3) heterogeneity analysis shows that the promotion effect is not related to geographical location, but the disadvantaged areas of enterprise digital transformation and regional green innovation efficiency have a greater impact. Further, the applicability of the research conclusions is extended through case studies in other countries. This study enriches the research perspective of the relationship between enterprise digital transformation and green innovation, and provides a new path for regional sustainable development.